The Atlantic rainforest is considered one of the most important hotspots of biodiversity on Earth. This great diversity results from the variation of climatic conditions (rainy, warm and cold in high mountains), what generates a unique series of rain forest ecosystems quite distinct from each other. Unfortunately, due to the human impact over the centuries, today there are just fragments of preserved native rainforest. During the investigation about the cyanobacterial flora from the Atlantic rainforest, a special Chamaesiphon morphotype was found on a rock in streaming water. Chamaesiphon stratosus sp. nova is close to C. britannicus (Fritsch) Komarek et Anagn., C. geitleri Luther and C. fuscus (Rostaf.) Hansg ., and differs from them mainly because of the cells disposition in one layer and exocytes liberation in a sheath at the upper part of cells. These two features belong to different subgenera of Chamaesiphon (Godlewskia and Chamaesiphonopsis). Thus, the Brazilian material displays features of both subgenera and puts in evidence the fragility of these characteristics at subgenus level. Therefore, a discussion about the taxonomy of these subgenera and a proposal for including Chamaesiphonopsis as a synonym of the Godlewskia were done.